3TTB

Structure of the Thioalkalivibrio paradoxus cytochrome c nitrite reductase in complex with sulfite

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SXQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	278	Protein solution (2.5mcl): 10mg/ml TvPaR, 0.05M Tris-HCl, pH8.0. Reservoir solution (2.5mcl): 0.02M cobalt chloride, 0.1M MES (pH 6.5), 1.8 M ammonium sulfate. The crystal was soaked in 0.05M sodium dithionite for 5 days, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.94	75.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.99	α = 90
b = 190.99	β = 90
c = 190.99	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2010-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.9779	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	39	100	0.122	16.53		155579	155516			33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.2	100		0.633	3.94		38451

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3SXQ	2	38.99	147798	7717	99.96	0.13505	0.1341	0.12	0.15298	0.12	RANDOM	22.994

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.929
r_dihedral_angle_4_deg	17.328
r_dihedral_angle_3_deg	13.986
r_dihedral_angle_1_deg	6.674
r_angle_refined_deg	1.699
r_scangle_it	0.969
r_mcangle_it	0.706
r_scbond_it	0.665
r_mcbond_it	0.4
r_chiral_restr	0.105

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8204
Nucleic Acid Atoms
Solvent Atoms	736
Heterogen Atoms	759

Software

Software
Software Name	Purpose
AUTOMAR	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.